CTU2

Summary

CTU2 (cytosolic thiouridylase subunit 2, HGNC:28005) is a protein-coding gene on chromosome 16q24.3, encoding Cytoplasmic tRNA 2-thiolation protein 2 (Q2VPK5). Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). It is a selective cancer dependency (DepMap: 77.8% of cell lines).

This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 348180 — RefSeq curated summary.

At a glance

• Gene–disease (curated): microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Strong, GenCC)
• GWAS associations: 9
• Clinical variants (ClinVar): 416 total — 8 pathogenic, 3 likely-pathogenic
• Phenotypes (HPO): 35
• Cancer dependency (DepMap): dependent in 77.8% of screened cell lines
• MANE Select transcript: NM_001012759

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28005
Approved symbol	CTU2
Name	cytosolic thiouridylase subunit 2
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Aliases	NCS2
Ensembl gene	ENSG00000174177
Ensembl biotype	protein_coding
OMIM	617057
Entrez	348180

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000312060, ENST00000453996, ENST00000562011, ENST00000564105, ENST00000564584, ENST00000564921, ENST00000565071, ENST00000566637, ENST00000567316, ENST00000567949, ENST00000869940, ENST00000869941, ENST00000869942, ENST00000869943

RefSeq mRNA: 4 — MANE Select: NM_001012759 NM_001012759, NM_001012762, NM_001318507, NM_001318513

CCDS: CCDS32506, CCDS45545, CCDS82026

Canonical transcript exons

ENST00000453996 — 15 exons

Exon	Start	End
ENSE00002581097	88706503	88706598
ENSE00003461988	88714587	88714737
ENSE00003464634	88713647	88713778
ENSE00003470369	88714860	88714926
ENSE00003475235	88709938	88710016
ENSE00003537233	88712622	88712905
ENSE00003594320	88712274	88712383
ENSE00003617315	88710223	88710282
ENSE00003629562	88715048	88715106
ENSE00003635889	88714383	88714486
ENSE00003649123	88707136	88707210
ENSE00003678100	88713312	88713447
ENSE00003679941	88714136	88714227
ENSE00003690024	88711635	88711695
ENSE00003848368	88715182	88715396

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 91.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.8785 / max 108.5483, expressed in 1766 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155547	10.8785	1766

Top tissues by expression

236 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	91.42	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.33	gold quality
gastrocnemius	UBERON:0001388	86.29	gold quality
left uterine tube	UBERON:0001303	85.98	gold quality
prefrontal cortex	UBERON:0000451	85.97	gold quality
apex of heart	UBERON:0002098	85.50	gold quality
right frontal lobe	UBERON:0002810	85.23	gold quality
muscle of leg	UBERON:0001383	85.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	84.58	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.45	gold quality
lower esophagus	UBERON:0013473	84.43	gold quality
anterior cingulate cortex	UBERON:0009835	84.32	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.28	gold quality
granulocyte	CL:0000094	84.20	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.07	gold quality
lower esophagus mucosa	UBERON:0035834	84.06	gold quality
right ovary	UBERON:0002118	83.98	gold quality
body of uterus	UBERON:0009853	83.91	gold quality
left coronary artery	UBERON:0001626	83.78	gold quality
cortical plate	UBERON:0005343	83.74	gold quality
left ovary	UBERON:0002119	83.68	gold quality
popliteal artery	UBERON:0002250	83.63	gold quality
tibial artery	UBERON:0007610	83.62	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.54	gold quality
omental fat pad	UBERON:0010414	83.41	gold quality
adenohypophysis	UBERON:0002196	83.39	gold quality
peritoneum	UBERON:0002358	83.38	gold quality
mucosa of transverse colon	UBERON:0004991	83.36	gold quality
right coronary artery	UBERON:0001625	83.32	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6142	no	77.71
E-ANND-3	no	2.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting CTU2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-1915-5P	95.25	65.78	571

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• Identifies the product of this gene as being involved in tRNA modification. (PMID:19017811)
• Our data establish a recognizable CTU2-linked autosomal recessive syndrome in humans characterized by defective thiolation of the wobble uridine. The potential deleterious consequences for the translational efficiency and fidelity during development as a mechanism for pathogenicity represent an attractive target of future investigations. (PMID:31301155)
• Activation of CTU2 expression by LXR promotes the development of hepatocellular carcinoma. (PMID:38630355)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ctu2	ENSDARG00000051851
mus_musculus	Ctu2	ENSMUSG00000049482
rattus_norvegicus	Ctu2	ENSRNOG00000051531
drosophila_melanogaster	Ctu2	FBGN0032793
caenorhabditis_elegans		WBGENE00009256

Protein

Protein identifiers

Cytoplasmic tRNA 2-thiolation protein 2 — Q2VPK5 (reviewed: Q2VPK5)

Alternative names: Cytosolic thiouridylase subunit 2

All UniProt accessions (5): Q2VPK5, H3BNM3, H3BNU5, H3BPG4, H3BSW6

UniProt curated annotations — full annotation on UniProt →

Function. Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wobble position.

Subunit / interactions. Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3.

Subcellular location. Cytoplasm.

Disease relevance. Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (MFRG) [MIM:618142] An autosomal dominant syndrome characterized by primary microcephaly, ambiguous male genitalia, dysmorphic facies, polydactyly, and unilateral renal agenesis. Variable brain, cardiac, and skeletal anomalies are present, including corpus callosum agenesis or dysgenesis, lissencephaly, atrial and ventricular septal defects, patent ductus arteriosus, hypoplastic right ventricle, and joint contractures. The disease may be caused by variants affecting the gene represented in this entry. A homozygous synonymous variant at codon 247 has been identified in 3 consanguineous families. This variant impairs normal splicing, causing a frameshift resulting in a premature termination codon.

Pathway. tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis.

Miscellaneous. Incomplete sequence.

Similarity. Belongs to the CTU2/NCS2 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q2VPK5-1	1	yes
Q2VPK5-3	2
Q2VPK5-5	3

RefSeq proteins (4): NP_001012777, NP_001012780, NP_001305436, NP_001305442 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR014729	Rossmann-like_a/b/a_fold	Homologous_superfamily
IPR019407	CTU2	Family

Pfam: PF10288

UniProt features (16 total): modified residue 5, sequence variant 4, splice variant 2, region of interest 2, initiator methionine 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2VPK5-F1	80.27	0.59

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 2, 415, 419, 435, 508

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6782315	tRNA modification in the nucleus and cytosol

MSigDB gene sets: 164 (showing top): GOBP_TRNA_METABOLIC_PROCESS, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, GOBP_RNA_MODIFICATION, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_TRNA_PROCESSING, REACTOME_METABOLISM_OF_RNA, GOBP_TRNA_MODIFICATION, GOMF_TRNA_BINDING, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_SULPHUR_CONTAINING_GROUPS, KARLSSON_TGFB1_TARGETS_UP, GOBP_TRNA_WOBBLE_BASE_MODIFICATION, KASLER_HDAC7_TARGETS_1_UP, GOBP_TRNA_THIO_MODIFICATION, VANOEVELEN_MYOGENESIS_SIN3A_TARGETS

GO Biological Process (5): tRNA wobble uridine modification (GO:0002098), tRNA wobble position uridine thiolation (GO:0002143), protein urmylation (GO:0032447), tRNA thio-modification (GO:0034227), tRNA processing (GO:0008033)

GO Molecular Function (4): tRNA binding (GO:0000049), nucleotidyltransferase activity (GO:0016779), sulfurtransferase activity (GO:0016783), protein binding (GO:0005515)

GO Cellular Component (3): cytosol (GO:0005829), protein-containing complex (GO:0032991), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
tRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
tRNA wobble base modification	1
tRNA wobble uridine modification	1
tRNA thio-modification	1
protein modification by small protein conjugation	1
tRNA modification	1
RNA processing	1
tRNA metabolic process	1
RNA binding	1
transferase activity, transferring phosphorus-containing groups	1
transferase activity, transferring sulphur-containing groups	1
binding	1
cytoplasm	1
cellular_component	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1302 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CTU2	CTU1	Q7Z7A3	991
CTU2	MOCS3	O95396	842
CTU2	NCS1	P36610	794
CTU2	URM1	Q9BTM9	757
CTU2	ELP3	Q9H9T3	709
CTU2	ALKBH8	Q96BT7	640
CTU2	TRMU	O75648	608
CTU2	NFS1	Q9Y697	575
CTU2	ELP6	Q0PNE2	571
CTU2	ELP2	Q6IA86	550
CTU2	MPST	P25325	507
CTU2	ELP5	Q8TE02	502
CTU2	TST	Q16762	500
CTU2	ELP4	Q96EB1	456
CTU2	TRMT5	Q32P41	450

IntAct

74 interactions, top by confidence:

A	B	Type	Score
ACBD6	NMT2	psi-mi:“MI:0914”(association)	0.870
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
PFDN4	PFDN6	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CCDC120	AIP	psi-mi:“MI:0914”(association)	0.640
CEP72	AHCYL1	psi-mi:“MI:0914”(association)	0.640
ZNF414	AHCYL1	psi-mi:“MI:0914”(association)	0.640
FLII	TMOD1	psi-mi:“MI:0914”(association)	0.640
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
RAB8B	BLTP3B	psi-mi:“MI:0914”(association)	0.530
SLC5A5	SLC19A2	psi-mi:“MI:0914”(association)	0.530
ZMAT5	DENND4B	psi-mi:“MI:0914”(association)	0.530
VASP	GTPBP1	psi-mi:“MI:0914”(association)	0.530
PBXIP1	KCNN4	psi-mi:“MI:0914”(association)	0.530
URM1	CTU2	psi-mi:“MI:0915”(physical association)	0.400
CTU1	HSPA1B	psi-mi:“MI:0914”(association)	0.350
TAFA3	FUOM	psi-mi:“MI:0914”(association)	0.350
PROSER2	VWA8	psi-mi:“MI:0914”(association)	0.350
KLHL20	KRBA1	psi-mi:“MI:0914”(association)	0.350
RGS20	PGP	psi-mi:“MI:0914”(association)	0.350

BioGRID (86): CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS), CTU2 (Affinity Capture-MS)

ESM2 similar proteins: A2VD13, A4D126, A5PK43, A6H751, A7E3N7, B0S6U7, B0S8I0, B5DFG1, D2GU20, E1BCH6, O75127, O75616, O95382, P36915, P36916, P48760, Q05932, Q2TBP8, Q2VPK5, Q3SZK4, Q3U269, Q3U5Q7, Q3V300, Q4R8D2, Q5E9Z1, Q5EBA0, Q5ND52, Q5QJC3, Q5R655, Q5RA07, Q5RJG7, Q5S6T3, Q5TM59, Q6MG06, Q7YR35, Q8C2E4, Q8CJ00, Q8JIF5, Q8K045, Q8NC60

Diamond homologs: A0NEF7, B0X911, B3MN57, B3NM45, B4GWY0, B4I5W3, B4JCV8, B4KIW3, B4M8J8, B4MYR2, B4PAZ6, B4Q9Z1, Q08B12, Q17JB7, Q28ES8, Q29K59, Q2VPK5, Q32NV1, Q3B7U4, Q3U308, Q9VIV3, Q3SZG9, Q55EX7, Q5BHB8, Q6DC53, B4HSL7, B4J5B3, B4NN33, Q6CF50, A1DDV3, B0Y1E7, Q4WVK2, A1CBI6, A3M0F4, A5DAK5, A5DSD3, A7F190, B2W6W8, Q0UDH1, Q2U667

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

416 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	8
Likely pathogenic	3
Uncertain significance	216
Likely benign	93
Benign	52

Top pathogenic / likely-pathogenic (11)

Variant ID	HGVS	Classification
4531303	CTU2, 1-BP DUP, 1206T	Pathogenic
4531304	CTU2, LEU63PRO	Pathogenic
4531305	CTU2, IVS4, G-A, +5	Pathogenic
4531306	CTU2, 4-BP DEL, 1514TTGA	Pathogenic
585016	NM_001012759.3(CTU2):c.873G>A (p.Thr291=)	Pathogenic
635409	NM_001012759.3(CTU2):c.1206dup (p.Ala403fs)	Pathogenic
635411	NM_001012759.3(CTU2):c.1514_1517del (p.Ile505fs)	Pathogenic
637954	NM_001012759.3(CTU2):c.282+5G>A	Pathogenic
1305419	NM_001012759.3(CTU2):c.453+1G>A	Likely pathogenic
1899145	NM_001012759.3(CTU2):c.1420-1G>A	Likely pathogenic
3357526	NM_001012759.3(CTU2):c.898del (p.Asp300fs)	Likely pathogenic

SpliceAI

2285 predictions. Top by Δscore:

Variant	Effect	Δscore
16:88706595:CCAGG:C	donor_loss	1.0000
16:88706596:CAGG:C	donor_loss	1.0000
16:88706597:AGG:A	donor_loss	1.0000
16:88706599:GTAAG:G	donor_loss	1.0000
16:88706600:T:A	donor_loss	1.0000
16:88707127:T:G	acceptor_gain	1.0000
16:88712158:G:GT	donor_gain	1.0000
16:88712381:G:GT	donor_gain	1.0000
16:88713641:CCGCA:C	acceptor_loss	1.0000
16:88713643:GCA:G	acceptor_loss	1.0000
16:88713644:CA:C	acceptor_loss	1.0000
16:88713645:A:AC	acceptor_loss	1.0000
16:88713645:A:AG	acceptor_gain	1.0000
16:88713645:AG:A	acceptor_gain	1.0000
16:88713646:G:GG	acceptor_gain	1.0000
16:88713646:G:GT	acceptor_loss	1.0000
16:88713646:GG:G	acceptor_gain	1.0000
16:88713646:GGGC:G	acceptor_gain	1.0000
16:88713713:G:GT	donor_gain	1.0000
16:88713775:CAAGG:C	donor_loss	1.0000
16:88713779:G:C	donor_loss	1.0000
16:88713779:G:GG	donor_gain	1.0000
16:88714370:AATCC:A	acceptor_gain	1.0000
16:88714374:C:CA	acceptor_gain	1.0000
16:88714471:G:GT	donor_gain	1.0000
16:88714856:GCAGG:G	acceptor_loss	1.0000
16:88714858:A:AG	acceptor_gain	1.0000
16:88714858:AG:A	acceptor_gain	1.0000
16:88714859:G:GA	acceptor_loss	1.0000
16:88714859:G:GG	acceptor_gain	1.0000

AlphaMissense

3326 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:88714151:A:C	S341R	0.995
16:88714153:C:A	S341R	0.995
16:88714153:C:G	S341R	0.995
16:88713422:G:C	R283P	0.994
16:88713373:A:C	S267R	0.992
16:88713375:C:A	S267R	0.992
16:88713375:C:G	S267R	0.992
16:88714199:T:C	F357L	0.992
16:88714201:C:A	F357L	0.992
16:88714201:C:G	F357L	0.992
16:88713335:C:A	A254D	0.991
16:88713359:T:A	V262D	0.991
16:88709969:T:C	F59L	0.990
16:88709970:T:C	F59S	0.990
16:88709971:C:A	F59L	0.990
16:88709971:C:G	F59L	0.990
16:88714175:T:C	F349L	0.990
16:88714177:C:A	F349L	0.990
16:88714177:C:G	F349L	0.990
16:88714227:G:C	R366T	0.989
16:88712890:T:C	L241P	0.988
16:88713687:G:C	R305P	0.988
16:88714221:T:A	V364E	0.988
16:88713419:G:T	G282V	0.986
16:88714227:G:T	R366M	0.986
16:88709963:C:G	H57D	0.985
16:88713398:T:C	L275P	0.985
16:88713419:G:A	G282D	0.985
16:88714188:T:C	L353P	0.985
16:88714383:G:C	R366S	0.985

dbSNP variants (sampled 300 via entrez): RS1000032798 (16:88711594 C>A,T), RS1000040633 (16:88706261 C>G,T), RS1000143981 (16:88708407 G>A,T), RS1000260545 (16:88708562 C>T), RS1000487579 (16:88711751 A>C,G), RS1000674828 (16:88704583 C>G,T), RS1000911929 (16:88714089 G>T), RS1000925279 (16:88715509 C>A,T), RS1001198804 (16:88711793 C>T), RS1001248096 (16:88711946 C>T), RS1001375714 (16:88707053 C>G,T), RS1001422093 (16:88710902 C>A,G,T), RS1001452762 (16:88704806 A>G), RS1001636501 (16:88714865 A>C,G), RS1001883722 (16:88708795 C>G,T)

Disease associations

OMIM: gene MIM:617057 | disease phenotypes: MIM:618142, MIM:610805

GenCC curated gene-disease

Disease	Classification	Inheritance
microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome	Strong	Autosomal recessive

Mondo (3): microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (MONDO:0020647), congenital anomaly of kidney and urinary tract (MONDO:0019719), microcephaly (MONDO:0001149)

Orphanet (1): Renal or urinary tract malformation (Orphanet:93545)

HPO phenotypes

35 total (30 of 35 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000054	Micropenis
HP:0000062	Ambiguous genitalia
HP:0000122	Unilateral renal agenesis
HP:0000218	High palate
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000278	Retrognathia
HP:0000316	Hypertelorism
HP:0000341	Narrow forehead
HP:0000347	Micrognathia
HP:0000369	Low-set ears
HP:0000400	Macrotia
HP:0000582	Upslanted palpebral fissure
HP:0001250	Seizure
HP:0001274	Agenesis of corpus callosum
HP:0001290	Generalized hypotonia
HP:0001339	Lissencephaly
HP:0001511	Intrauterine growth retardation
HP:0001629	Ventricular septal defect
HP:0001631	Atrial septal defect
HP:0001643	Patent ductus arteriosus
HP:0001776	Bilateral talipes equinovarus
HP:0001845	Overlapping toe
HP:0002079	Hypoplasia of the corpus callosum
HP:0002280	Enlarged cisterna magna
HP:0002553	Highly arched eyebrow
HP:0003577	Congenital onset
HP:0004736	Crossed fused renal ectopia
HP:0005280	Depressed nasal bridge

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST002639_1	Autism spectrum disorder-related traits	3.000000e-07
GCST003479_9	Hair color	1.000000e-07
GCST004607_66	Plateletcrit	3.000000e-10
GCST004612_201	High light scatter reticulocyte percentage of red cells	4.000000e-14
GCST004619_180	Reticulocyte fraction of red cells	5.000000e-16
GCST005024_98	Pursuit maintenance gain	4.000000e-06
GCST012226_390	Waist circumference adjusted for body mass index	6.000000e-09
GCST90002384_395	Hemoglobin	3.000000e-09
GCST90020028_1502	Hip circumference adjusted for BMI	8.000000e-09

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0005426	autism spectrum disorder symptom
EFO:0007985	platelet crit
EFO:0007986	reticulocyte count
EFO:0008433	pursuit maintenance gain measurement
EFO:0007789	BMI-adjusted waist circumference
EFO:0004509	hemoglobin measurement
EFO:0008039	BMI-adjusted hip circumference

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008831	Microcephaly	C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
C566906	Cakut (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	2
FR900359	increases phosphorylation	1
bisphenol A	decreases methylation	1
sodium arsenite	decreases expression	1
cobaltous chloride	increases expression	1
aflatoxin B2	decreases methylation	1
bisphenol S	decreases methylation	1
Sunitinib	increases expression	1
Zoledronic Acid	decreases expression	1
Vehicle Emissions	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Calcitriol	decreases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Doxorubicin	decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Thiram	decreases expression	1
Valproic Acid	increases methylation	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

21 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT04115345	PHASE1	COMPLETED	A Study of a Renal Autologous Cell Therapy (REACT) in Patients With Chronic Kidney Disease (CKD) From Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
NCT05694169	PHASE1	TERMINATED	A Study of Participants With Chronic Kidney Disease Previously Treated With REACT
NCT04537364	Not specified	COMPLETED	Prediction of Renal Parenchymal Damage of CAKUT
NCT06921733	Not specified	RECRUITING	Ultrasound Localization Microscopy in Patient With Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)
NCT05518188	PHASE1/PHASE2	RECRUITING	Melpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT00001639	Not specified	COMPLETED	Evaluation of Patients With Unresolved Chromosome Abnormalities
NCT01151462	Not specified	WITHDRAWN	Postnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
NCT01565005	Not specified	COMPLETED	Microcephaly Genetic Deficiency in Neural Progenitors
NCT02510170	Not specified	COMPLETED	Fetal and Maternal Head Circumference During Pregnancy in Israeli Population
NCT02741882	Not specified	COMPLETED	Zika and Microcephaly: Case-control Study
NCT02943304	Not specified	COMPLETED	Neurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero
NCT03255369	Not specified	UNKNOWN	Vertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF)
NCT03325946	Not specified	RECRUITING	The FBRI VTC Neuromotor Research Clinic
NCT03330600	Not specified	COMPLETED	Efficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome
NCT03548779	Not specified	COMPLETED	North Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
NCT03651687	Not specified	COMPLETED	Guangzhou Surveillance and Clinical Study in Microcephaly (GSCSM)
NCT03922594	Not specified	TERMINATED	Surveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia
NCT04816175	Not specified	COMPLETED	Intensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay
NCT05322980	Not specified	COMPLETED	Summary of Infants Weighing 500 Grams or Less
NCT06019182	Not specified	RECRUITING	MEHMO Natural History and Biomarkers
NCT06566066	Not specified	RECRUITING	Register for Patients With Thyroid Hormone Resistance.